Permanent Changes
by AlexaNDYE
Summary: Killian surprises Tony Stark by releasing their hostage, Pepper Potts, but when he finds her, he is hit with a horrific sight, changing both their lives dramatically and permanently. WARNING: THIS FANFIC CONTAINS MAJOR SPOILERS ABOUT IRON MAN 3 THAT MAY OR MAY NOT BE TRUE. PLEASE READ AT YOUR OWN RISK.


Title: Permanent Changes

Rated: T

Category: Hurt/Comfort, Drama

WARNING: MAJOR SPOILERS THAT MAY OR MAY NOT BE TRUE. READ AT YOUR OWN RISK.

The spoilers that are mentioned in this fanfic: Happy is dead, Pepper has an unstable Arc Reactor forced on her by A.I.M, Tony fixes her Arc Reactor, and Pepper's leave for some time to herself.

A few days after the Mandarin had attacked, and destroyed, his beautiful Malibu home, Tony Stark found himself threatened by the very man himself. The Mandarin hadn't threatened to kill him, nor did he threaten to destroy the planet. He threatened Tony with the very life of his part time Personal Assistant, Co-CEO, and girlfriend, Pepper Potts. Tony felt his heart beat faster, knowing that her life was in danger. No doubt, Killian was the one that took her and held her against her will.

Tony didn't want to even think of the things they were doing to her. It took all of his willpower to not storm the front and take her back by force. He even asked Rhodey what he should do, and they both had the same thoughts; wait until a proper plan is thought out. Tony couldn't remember how many days he went, trying to devise a plan. It felt like two, maybe two and a half, days since The Mandarin told him of his hostage.

What had happened next made Tony's Arc Reactor buzz; the feeling of being completely empty and utterly useless rushed through him. Killian had called him, and Tony did the usual routine by prompting JARVIS to trace the call. When Killian told Tony of a location, Tony thought he was a stupid half wit, but Killian started to laugh.

"This isn't a house call, Stark. I'm not calling you simply to beat you at your own game." Killian said in a cold voice before pausing. "We're releasing your lovely assistant. Hopefully you have a better time than we did."

Tony screamed, asking what they did to her. Tony swore he heard a smile through the phone. Killian didn't respond with an answer; he only repeated the address before hanging up.

Tony called his armor to him using the Extremis and rushed out of a secret cave he had used as an alternative workshop after his beautiful Malibu house was destroyed.

"JARVIS." He called to his AI.

"Yes, Sir?" His AI responded.

"Input the exact coordinates. I'm going to need an ETA."

"Coordinates uploaded." JARVIS announced. Tony saw a mini map show up on his HUD with a little blinking light that pinpointed his exact location. "ETA is twelve minutes."

Tony, determined with all of his power to rescue Pepper, angrily gritted his teeth. "Make that one minute."

He landed in a remote area; there were trees, a lot of trees. The dark night only made it worse because he couldn't see through the thick forest. In the distance, he heard a whirling. It sounded a lot like a helicopter, and he was right. To the right of him was the sight of a helicopter taking off. His HUD allowed him to zoom in. Killian was standing near the edge with a sly smile on his face. Before the helicopter was out of range, he saw Killian give him one last salute, no doubt taunting him and his abilities as a superhero.

"Where is she?" Tony asked frantically. His breathing soon became erratic to the point where he could've sworn he stopped breathing.

"My sensors are picking up signals one point five miles to your right." JARVIS responded.

Flying would be pointless, so Tony ran through the forest in his Mark XLVII suit, trying to keep his emotions together to prevent the Extremis from releasing the armor off his body. As he got closer, he could hear her cries of pain. He could hear how scared she was and it frightened him. He slowed down, and walked through three layers of thick trees before staring at the most horrible and frightening sight he had ever seen in his life.

Pepper was lying on the ground. Her white dress shirt, the one she wore at the time of the attack on his Malibu home, was splattered with blood, no doubt her own. He was frozen in his place, trying to process everything that he was seeing.

When he could finally urge himself to move, he whispered, "No" and seconds later whispered her name. As he ran towards her side, his emotions got in the way of the Extremis, and as he took off his helmet, he released his gauntlets as well. He kneeled in front of her blood stained body, and practically shook with fear.

"Pepper." He murmured, carefully skimming her body with his hand and his eyes. He couldn't bring himself to even look at her, but when he finally did, he saw tears flowing from her eyes in what seemed a never ending stream.

She writhed on the ground, trying to stifle back her screams of pain. "Tony." She managed to breathe. Her eyes opened slightly but closed again due to the unbearable pain. "Ah!" She screamed.

"The device is unstable." JARVIS suddenly announced from his discarded helmet.

It took Tony a few minutes to register what his AI said only because he couldn't stop staring at her blood stained body. He reached out to grasp her hand, comforting her with his presence. "What?" He furrowed his eyebrows.

"The Reactor Core is unstable." The AI repeated.

What he saw felt like he was punched in the chest by the Hulk. "No." He murmured shakily. He let go of her hand and quickly drew back the top of her dress shirt. He wanted to scream—he wanted to yell from the top of his lungs. He was never prepared to see this.

"Oh god." He gasped, trying to fight back the tears that were breaching the corners of his eyes. He clasped his hand over his mouth, trying not to scream; he could only take deep breaths through his nose, "Pepper—". It felt like he couldn't move. "—What the hell did they do to you?"

"Ah!" Pepper yelled again. Her finger nails dug into the soil beside her, trying to fight back the pain as the Arc Reactor in her chest began to blink and spark.

"Shit!" Tony swore to himself. He grabbed his helmet and hurriedly put it on. He looked through his HUD as JARVIS inspected the device, and saw numerous missing parts and the wrong number of cycles.

"The unstable device in Miss Potts' chest—if left unattended, it will—"

"I know." Tony spat back, trying to hold his emotions together. He quickly threw his hands outward and called his gauntlets back to him. After they zipped onto his hands, layering along his wrists, they locked into place with the armor that protected the rest of his forearm. He wished he could tell her what his heart was telling him to say—he loves her, he's sorry, and he wished this never happened to her—but right now, he was more concerned with her life.

He hated it how his suit makes his voice stone cold and emotionless. "Pepper," His breath was still erratic. "I'm going to fix this". His hands wrap around her shoulders and underneath her legs. Pepper, letting go of the soil surrounding her body, desperately grabbed onto his armor near his neck. His heart almost gave out when he saw her shiver from the cold breeze that continuously passed; she clung onto him in search of warmth, warmth he couldn't give her at the moment. "Hang on." He told her worriedly. "Everything's going to be okay, Pepper." He tried to comfort her one last time before he shot up into the sky.

Tony got back to the cave in record time. He hurried into the cave, barking access codes that moved panels around so that he could access his secret workshop. As he walked towards an empty metal observation table, and as his emotions ran wild, the Extremis let parts of his suit fall on the ground. Individual parts were lying strewn across the workshop; the last parts were his gauntlets and his helmet. He laid Pepper on top of the table, and when he had finally taken off the rest of his suit, he immediately grasped her hand with his, comforting her – telling her that he was there.

He stared at her with worried eyes. "JARVIS." He barked orders. "Scan her Arc Reactor. I want to know exactly what those assholes put in her chest."

"Scanning." JARVIS responded rather quickly.

He tightened his hold on her hand, watching the tears flow out from the corner of her eyes. "It's going to be okay, Pepper." He tried to comfort her; he laid his forehead against her bloodstained clothed shoulder and tried as hard as he could to fight back the tears that were threatening to escape.

Pepper kept moving her body uncontrollably; the pain from the unstable reactor was starting to get worse. She wasn't screaming anymore; she was biting her bottom lip and gripping his hand as hard as she could. His lips quivered as he tried his best to stay strong for her. He looked down at her black jeans – he couldn't tell if they too were covered in blood and it scared him.

"Scanning complete." His AI announced. Tony gave Pepper's hand one last squeeze before letting go. He walked around to one of the thin glass panels and activated it with the touch of his finger. He slid around a few things before bringing up the main part of his focus. He looked at the diagram that JARVIS had generated when he scanned Pepper's chest.

The thing that shocked him the most was how wrong it was—it was all wrong; the design, the number of cycles, the materials they used for the reactor core as well as the materials used to hold it all together—all of it seemed like a poor attempt at creating a duplicate of his Arc Reactor.

Tony's mouth gapped when he finally understood everything. He turned his head towards Pepper's shaking body on the metal observation table and drew a sharp breath. "They used you… they used you as an experiment…" He shook his head in disbelief and disappointment. "They used you as a tool to test a poor excuse of an Arc Reactor—they… used—" He banged his hand on the table beside him in an angry rage and began to choke back tears.

"The Arc Reactor can be fixed, but in order for Miss Potts to survive, there needs to be a substitute." JARVIS told him.

"I know." Tony muttered coldly. He turned to a box of scraps he salvaged from the wreck of his Malibu home, and took out a car battery. He reached inside the box of scraps again and took out an old Arc Reactor, one he scrapped a while ago. He made a few modifications and combined the two; it brought back a lot of memories, as it was the same Arc Reactor he woke up with in the cave in Afghanistan.

He hurried over to Pepper and spun it counterclockwise, unlocking the RT. "You're going to feel an uncomfortable sensation for a few moments." He told her. Pepper held onto fabric of his under armor shirt in response. He reached inside the metal cylinder in her chest and unplugged the Arc Reactor from the base plate. Pepper's breathing began to quicken, as if she was gasping for air. Tony expected that reaction; he quickly attached the battery powered Arc Reactor to her base plate and watched as she settled down.

The good news was that her life was no longer in danger, but the bad news was that her life was now running on reserved power. The car battery could only last so long, which meant that he had to work fast. He looked down at his girlfriend, trying his best to ignore the blood splatters across her dress shirt, and gently rubbed her shoulder with his free hand, comforting her and himself.

"You'll be okay, Pepper." He smiled weakly. Pepper could only stare at him in belief. "I promise." He bent over and kissed her on the forehead. He thought she was exhausted from her traumatic experience and was going to rest, but she didn't. She watched him work on her, now called, heart.

Her arms slowly trailed up the side of her body and towards the gaping whole in her chest. She felt around, feeling the wires of the attached car battery, and the greasy old temporary Arc Reactor. It felt weird—it felt like she was touching her own organs. She felt pain; it hurt but she wasn't sure if it was from the new whole in her chest or from her aching heart. She didn't blame him. No. She could never blame him for what happened to her. She knows that he blames himself. She didn't hate him, she loved him, but at that point, she wasn't sure if she could ever feel safe around him.

She tilted her head to the side and silently watched Tony work. Her vision went hazy a few times, and the only parts she saw was when he took apart the Arc Reactor, added some new parts and configured it, and put it back together. Suddenly, her vision went normal and her breathing became regular. Her curiosity got the better of her; she opened her eyes and looked down at her chest. Tony had replaced the substitute with a fixed version of her Arc Reactor.

"It's no longer unstable." He managed to choke out.

Pepper, with all of her strength and with the help of Tony, sat up. She didn't say anything; she didn't cry and she didn't look at him. She could only stare down at the bright blue glowing Arc Reactor in the center of her chest. She touched it softly, observing the curves, edges, and the faint humming noise it emitted. It sounded like his.

"It should be better now." Tony broke the silence.

Pepper slowly tilted her head up to stare at him. He could tell, through her ocean blue eyes, that she was in more pain than she could handle. It wasn't physical pain – it was mental and emotional pain.

He shoved himself at her and desperately clung onto her body, holding on to her for dear life; it was something he had wanted to do since he found her. He choked out quiet sobs as he held her against his chest. His world was crumbling down on him at once; he could no longer hold in all the emotional stress. Pepper could only grab a fist full of his under armor in her hands, force her eyes closed, and silently take in everything that had happened.

"I thought I lost you, Pepper." Tony managed to gasp. "God, I'm so sorry." She could feel his tears drip on the shoulder of her bloodstained dress shirt. "Pepper." He cried out.

It took him a while to settle down, only because he felt like if he ever let go of her, he would never see her again. When Tony finally released her hold on her, he looked down at her clothes and immediately led her to a twin sized bed in the back of the workshop. He made a joke about how it was more comfortable than the one in their Malibu home. Pepper responded with a small smile, and nothing more. It surprised her to see that he managed to stash some of her clothes in this makeshift cave slash secret workshop. He handed her a plain grey t-shirt and a pair of sweats. Pepper wordlessly dressed herself in fresh clothes. Her silent actions worried him. Could she even bring herself to look at him? Did she hate him? Did she not want to talk to him because of what happened to her? Did she blame him? All these questions ran through his head as he watched her hunched over form on top of the bed.

Tony didn't change out of his clothes. He was too worried about her to even think about eating – which reminded him—"Did you want something to eat?" He asked her, sitting down on the bed next to her.

She didn't look at him. She only shook her head.

"Pepper." He whispered. "Say something." His eyes were filled with sadness. "You don't have to tell me that you blame me. I already know."

"I don't blame you, Tony." She muttered, making him whip his head up to stare at her with a shocked expression.

"How could you not?" He asked, trying to understand. "If it weren't for me, you wouldn't have that _thing_ in your chest." He gestured towards the Arc Reactor that glowed through her t-shirt.

"I knew what I was getting into when we entered this relationship—" She tried to calmly tell him.

"Yeah, I know that, but getting captured and being experimented on, with a poor excuse for an Arc Reactor, isn't part of the commitment." He began to raise his voice.

"Tony—"

"No." He shook his head before he stood up. "I'm stupid." He told her, staring down at her. Pepper could only frown up at him, unsure of what to say. "I'm stupid to ever think that this could work out, because who am I kidding, how could I ever protect you from the hundreds and hundreds of people that want me dead?"

He held back a few tears as his bottom lip began to quiver.

"I'm not supposed to be alive, Pepper. How I survived is still beyond me."

Pepper stood up with the best of her ability and held his face in her hands, trying to calm him down. "Stop it, Tony." She murmured. "You're alive for a reason. It wasn't luck that brought you out of that cave and to me." Tony shook his head at her, but Pepper made him listen. "I love you. No matter how stupid, idiotic, or selfish you are, I will _always_ love you. And a part of me wants to blame this whole thing on you, but what good does that do? I would be only lying to myself, because it's not your fault, Tony. It's their fault. They're the ones that did this to me, not you."

Tony closed his eyes, letting a few tears roll down his cheek. He held onto her hands and buried his face deeper into her hold.

"I'm sorry." He gasped. "I'm sorry, Pepper. I'm sorry this happened to you—it shouldn't have—it shouldn't—"

"Shhh." She shushed him, trying to calm him down.

She moved him back onto the bed and laid them down. They talked for a little less than an hour, mourning Happy's death and comforting each other through all of the terrible events that have been occurring. He held her against him as tight as she would allow him. He wasn't being possessive, he was just being protective, because the one thing he wanted to do is protect the one thing he couldn't live without.

Deep down, Pepper was exhausted, and desperately needed some sleep, but that didn't mean she could just easily forget what happened. It was a huge traumatic experience for her, and it surprised her that she kept the uneasy feeling in the pit of her stomach and her mind.

She lay there for a couple hours, unsure of her future. What could she do with a bright glowing circle in the middle of her chest?

"You okay?" His voice pulled her out of her deep thoughts. She was so lost in her own thoughts that she didn't even pick up on his very noticeable stare.

"Yeah." She managed to gasp. His arm was wrapped around her middle, and his head was resting on her shoulder.

"What's wrong?" He asked again.

Pepper stayed silent for a few moments. She didn't want to lie to him, nor did she want to push him away as if he couldn't do anything to help her.

"What am I supposed to do now?" She asked him.

"Is this a trick question?" He asked playfully, furrowing his eyebrows.

"Our Malibu home is gone, Tony. Happy is dead, and everything is turning a wrong corner. I don't even know if there _will_ be a Stark Industries to manage after all this ends." He could hear the stress in her voice. It always pained him to see her stressed out.

"Nothing will be the same but…" He paused. "Everything will be fine , Pepper." He tried to comfort her.

"How do you know that?" She turned her head to look at him in the eyes. "If people find out that _this_ happened to me," She gestured towards her chest. "People are going to start asking questions, and then the media is going to be all over me—I just don't know if I can take it anymore."

"What do you mean by that?" He asked her intently.

Pepper buried her face in her hands and shook her head. "I don't know." She shook her head again and lay there for a few minutes, trying to think of her future. "I don't know, Tony." She told him again. "I need time to figure this out."

"You shouldn't get ahead of yourself, Pepper. There's no telling how this whole thing could turn out." He tried to tell her; he pressed a light kiss to the side of her head. "You should get some rest now and worry about it tomorrow."

She pressed her lips together; she was fighting with herself because the next few words had to be carefully thought out. "This isn't some Charity Ball that comes and goes, Tony. This is my future—this is the rest of my life." She paused. "The rest of my life will be revolving around this thing in my chest, this thing that I never asked for."

Her words hit him like a ton of bricks. "I know", is all he could say.

"I'm not you, Tony." She said rather harshly. "But this thing… This thing is forcing me to be _you_." She felt Tony's hold on her stomach tighten, which meant that he knew where she was going with this—she wanted time to herself, she wanted to get away from all this craziness. "I'm not a super hero. I'm a business woman. I am—or I was—Co-CEO of Stark Industries, but all that could change because of—" She stopped short, because they both knew what she was referring to.

"What do you want me to tell you, Pepper?" He said arguably. "You can't magically whisk your Arc Reactor away just because you want it gone. It doesn't work like that."

"Then tell me, Tony. Tell me what I should do." She snapped back at him.

He released his hold on her middle. "What do _you_ want to do?"

"I want to leave." She blurted without thinking.

"Leave for vocation…?" He furrowed his eyebrows at her.

"No." She paused, unable to look at him. "I want to leave… I want some time to myself—to think over what I should do."

"No. You're not leaving." He shook his head. "Not while the Mandarin and that jackass Killian are still out there."

She stood up from the bed and began to shout at him. "Do you know how traumatic it's been for me, Tony!?" Tears were rolling down her cheeks as she yelled. "I could feel everything they did to me! They cut me open, shoved this _thing_ inside of me, ran some tests on me as if I were a lab rat, and dumped me in the forest as if I were a failed experiment!" Tony could only stare up at her with sympathy. "Do you know how much I've wanted to yank out this _thing_!? I _hate_ it, Tony! I _don't_ blame you for this, but _I _am not _you_, Tony! Don't tell me what I should do because you don't know how I feel!"

Tony stood up from the bed as well, enraged by her words. "I know how you feel, Pepper!" He yelled back. "You want to know how!?" He paused to let her respond, but she never did. "Because the same thing happened to me in that hell hole in Afghanistan! They cut me open, shoved a magnet in my chest, and attached it to some old car battery!" Pepper was tearing up at this point, not because she forgot how he winded up with an Arc Reactor in the first place, but because they were more alike now than ever. She asked herself how he even survived after Afghanistan because she could barely deal with everything that's been happening to her.

His he spoke in a calm voice now. "I'm sorry this happened to you. I'm sorry that I couldn't stop it from happening and I'm sorry that I'm such a horrible boyfriend that I couldn't even protect you. But I promise, Pepper, I promise to help you through this." He stepped towards her and took her hands in his. "Please… don't leave," He planted a soft kiss on her hands. "You shouldn't have to deal with this alone." Pepper rested her head against his chest in defeat and Tony embraced her endearingly.

She cried against his chest, soaking his under armor. He could feel every tear that his shirt absorbed, because he had the same tears. They were never physical, they were always mental. He shielded his emotions and kept them in a silver box, unopened and untouched, until Pepper came along and opened the box for him, carefully and delicately going through the items.

He owed her his life. He always wondered if he could ever repay her back.

"I love you, Pepper."


End file.
